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Open data
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Basic information
Entry | Database: PDB / ID: 7c7e | ||||||
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Title | Crystal structure of C terminal domain of Escherichia coli DgoR | ||||||
![]() | Putative DNA-binding transcriptional regulator | ||||||
![]() | DNA BINDING PROTEIN / D-galactonate / GntR superfamily / transcription repressor | ||||||
Function / homology | ![]() | ||||||
Biological species | Escherichia coli O7:K1 | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lin, W. | ||||||
![]() | ![]() Title: Structural and Functional Analyses of the Transcription Repressor DgoR From Escherichia coli Reveal a Divalent Metal-Containing D-Galactonate Binding Pocket. Authors: Lin, Z. / Sun, Y. / Liu, Y. / Tong, S. / Shang, Z. / Cai, Y. / Lin, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 41 KB | Display | ![]() |
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PDB format | ![]() | 30.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 7.9 KB | Display | |
Data in CIF | ![]() | 9.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 26485.758 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: dgoR, ECIAI39_4297 Production host: ![]() ![]() References: UniProt: A0A0H3MRW3 |
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#2: Chemical | ChemComp-ZN / |
#3: Chemical | ChemComp-SO4 / |
#4: Chemical | ChemComp-PGE / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.9 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 5% PEG 400, 100mM Sodium acetate pH 5.5, 2M Lithium sulfate, 100mM Magnesium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 27, 2019 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.04→73.65 Å / Num. obs: 15623 / % possible obs: 100 % / Redundancy: 20 % / CC1/2: 1 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.015 / Rrim(I) all: 0.093 / Net I/σ(I): 34.6 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 120.31 Å2 / Biso mean: 54.1432 Å2 / Biso min: 25.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.047→28.01 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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